PeptideClassifier for protein inference and targeted quantitative proteomics

被引:72
作者
Qeli, Ermir [1 ]
Ahrens, Christian H. [1 ]
机构
[1] Univ Zurich, Inst Mol Life Sci, CH-8057 Zurich, Switzerland
关键词
TANDEM MASS-SPECTROMETRY; DROSOPHILA-MELANOGASTER; IDENTIFICATIONS; SENSITIVITY; CATALOG; PEPTIDE; YEAST;
D O I
10.1038/nbt0710-647
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
引用
收藏
页码:647 / 650
页数:4
相关论文
共 15 条
[1]   A Proteome Catalog of Drosophila melanogaster -: An essential resource for targeted quantitative proteomics [J].
Ahrens, Christian H. ;
Brunner, Erich ;
Hafen, Ernst ;
Aebersold, Ruedi ;
Basler, Konrad .
FLY, 2007, 1 (03) :182-186
[2]   A Human Proteome Detection and Quantitation Project [J].
Anderson, N. Leigh ;
Anderson, Norman G. ;
Pearson, Terry W. ;
Borchers, Christoph H. ;
Paulovich, Amanda G. ;
Patterson, Scott D. ;
Gillette, Michael ;
Aebersold, Ruedi ;
Carr, Steven A. .
MOLECULAR & CELLULAR PROTEOMICS, 2009, 8 (05) :883-886
[3]   A high-quality catalog of the Drosophila melanogaster proteome [J].
Brunner, Erich ;
Ahrens, Christian H. ;
Mohanty, Sonali ;
Baetschmann, Hansruedi ;
Loevenich, Sandra ;
Potthast, Frank ;
Deutsch, Eric W. ;
Panse, Christian ;
de Lichtenberg, Ulrik ;
Rinner, Oliver ;
Lee, Hookeun ;
Pedrioli, Patrick G. A. ;
Malmstrom, Johan ;
Koehler, Katja ;
Schrimpf, Sabine ;
Krijgsveld, Jeroen ;
Kregenow, Floyd ;
Heck, Albert J. R. ;
Hafen, Ernst ;
Schlapbach, Ralph ;
Aebersold, Ruedi .
NATURE BIOTECHNOLOGY, 2007, 25 (05) :576-583
[4]   The need for guidelines in publication of peptide and protein identification data - Working group on publication guidelines for peptide and protein identification data [J].
Carr, S ;
Aebersold, R ;
Baldwin, M ;
Burlingame, A ;
Clauser, K ;
Nesvizhskii, A .
MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (06) :531-533
[5]   Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast [J].
de Godoy, Lyris M. F. ;
Olsen, Jesper V. ;
Cox, Juergen ;
Nielsen, Michael L. ;
Hubner, Nina C. ;
Froehlich, Florian ;
Walther, Tobias C. ;
Mann, Matthias .
NATURE, 2008, 455 (7217) :1251-U60
[6]   Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry [J].
Elias, Joshua E. ;
Gygi, Steven P. .
NATURE METHODS, 2007, 4 (03) :207-214
[7]   Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function [J].
Grobei, Monica A. ;
Qeli, Ermir ;
Brunner, Erich ;
Rehrauer, Hubert ;
Zhang, Runxuan ;
Roschitzki, Bernd ;
Basler, Konrad ;
Ahrens, Christian H. ;
Grossniklaus, Ueli .
GENOME RESEARCH, 2009, 19 (10) :1786-1800
[8]   False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule [J].
Gupta, Nitin ;
Pevzner, Pavel A. .
JOURNAL OF PROTEOME RESEARCH, 2009, 8 (09) :4173-4181
[9]   IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering [J].
Ma, Ze-Qiang ;
Dasari, Surendra ;
Chambers, Matthew C. ;
Litton, Michael D. ;
Sobecki, Scott M. ;
Zimmerman, Lisa J. ;
Halvey, Patrick J. ;
Schilling, Birgit ;
Drake, Penelope M. ;
Gibson, Bradford W. ;
Tabb, David L. .
JOURNAL OF PROTEOME RESEARCH, 2009, 8 (08) :3872-3881
[10]   Interpretation of shotgun proteomic data - The protein inference problem [J].
Nesvizhskii, AI ;
Aebersold, R .
MOLECULAR & CELLULAR PROTEOMICS, 2005, 4 (10) :1419-1440